On 9/25/13 2:43 AM, Magdalena Schacherl wrote: > Dear fink programmers, > I have encountered the following problem when updating fink packages: > > Linking CXX static library libGraphMol_static.a > > [ 37%] Built target GraphMol_static > > [ 38%] [FLEX][SmartsL] Building scanner with flex 2.5.35 > > [ 38%] [BISON][SmilesY] Building parser with bison 3.0 > > smiles.yy:1.1-12: Warnung: deprecated directive, use „%pure-parser“ > [-Wdeprecated] > > %pure_parser > > ^^^^^^^^^^^^ > > [ 38%] [BISON][SmartsY] Building parser with bison 3.0 > > smarts.yy:1.1-12: Warnung: deprecated directive, use „%pure-parser“ > [-Wdeprecated] > > %pure_parser > > ^^^^^^^^^^^^ > > smarts.yy: Warnung: 86 shift/reduce conflicts [-Wconflicts-sr] > > [ 38%] [FLEX][SmilesL] Building scanner with flex 2.5.35 > > Scanning dependencies of target SmilesParse > > [ 38%] Building CXX object > Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o > > [ 38%] Building CXX object > Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o > > [ 38%] Building CXX object > Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o > > [ 39%] Building CXX object > Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o > > [ 39%] Building CXX object > Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o > > smiles.yy:25:1: warning: "YYDEBUG" redefined > > In file included from smiles.yy:21: > > /sw64/src/fink.build/rdkit-2013.06.1-5/RDKit_2013_06_1/Code/GraphMol/SmilesParse/smiles.tab.hpp:37:1: > warning: this is the location of the previous definition > > smiles.yy: In function 'int yysmiles_parse(const char*, > std::vector<RDKit::RWMol*, std::allocator<RDKit::RWMol*> >*, > std::list<unsigned int, std::allocator<unsigned int> >*, void*)': > > smiles.yy:23: error: too few arguments to function 'int > yysmiles_lex(YYSTYPE*, void*)' > > /sw64/src/fink.build/rdkit-2013.06.1-5/RDKit_2013_06_1/Code/GraphMol/SmilesParse/smiles.tab.cpp:1245: > error: at this point in file > > make[2]: *** > [Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o] > Error 1 > > make[1]: *** [Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all] > Error 2 > > make: *** [all] Error 2 > > ### execution of /tmp/fink.tFAYE failed, exit code 2 > > ### execution of /tmp/fink.35L3b failed, exit code 2 > > Removing runtime build-lock... > > Removing build-lock package... > > /sw64/bin/dpkg-lockwait -r fink-buildlock-rdkit-2013.06.1-5 > > (Reading database ... 220471 files and directories currently installed.) > > Removing fink-buildlock-rdkit-2013.06.1-5 ... > > Failed: phase compiling: rdkit-2013.06.1-5 failed > > Package manager version: 0.35.1 > > Distribution version: selfupdate-cvs Wed Sep 25 10:20:40 2013, 10.6, x86_64 > > Trees: local/main stable/main stable/crypto unstable/main unstable/crypto > > Xcode.app: 3.2.6 > > Xcode command-line tools: 3.2.6 > > Max. Fink build jobs:1 > > > > I have updated fink via selfupdate, but the problem persists. > > Thank you for your help. > > Kind regards, > Magdalena > > --------------------------- > Magdalena Schacherl, Ph.D. > Cologne University > Institute of Biochemistry > Structural biology / Group Prof. Baumann > Otto-Fischer-Str. 14 > 50674 Köln > Germany > > +49 221 470 3212 (phone) > +49 221 470 5066 (fax) > [email protected] <mailto:[email protected]> > www.px.uni-koeln.de <http://www.px.uni-koeln.de> > > >
Try removing Fink's bison--it appears to be too new. I saw the same error with Fink's bison installed, and removing it allowed the build to continue. -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk _______________________________________________ Fink-users mailing list [email protected] List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
